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Q9SHE7 (RUB1_ARATH) Reviewed, UniProtKB/Swiss-Prot

Last modified July 9, 2014. Version 101. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (3) | Third-party data text xml rdf/xml gff fasta
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Names and origin

Protein namesRecommended name:
Ubiquitin-NEDD8-like protein RUB1

Cleaved into the following 2 chains:

  1. Ubiquitin
  2. NEDD8-like protein RUB1
    Alternative name(s):
    Ubiquitin-related protein 1
    Short name=AtRUB1
Gene names
Name:RUB1
Synonyms:NEDD8, UBQ15
Ordered Locus Names:At1g31340
ORF Names:T19E23.13
OrganismArabidopsis thaliana (Mouse-ear cress) [Reference proteome]
Taxonomic identifier3702 [NCBI]
Taxonomic lineageEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliophytaeudicotyledonsGunneridaePentapetalaerosidsmalvidsBrassicalesBrassicaceaeCamelineaeArabidopsis

Protein attributes

Sequence length156 AA.
Sequence statusComplete.
Sequence processingThe displayed sequence is further processed into a mature form.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

Ubiquitin exists either covalently attached to another protein, or free (unanchored). When covalently bound, it is conjugated to target proteins via an isopeptide bond either as a monomer (monoubiquitin), a polymer linked via different Lys residues of the ubiquitin (polyubiquitin chains) or a linear polymer linked via the initiator Met of the ubiquitin (linear polyubiquitin chains). Polyubiquitin chains, when attached to a target protein, have different functions depending on the Lys residue of the ubiquitin that is linked: Lys-11-linked is involved in ERAD (endoplasmic reticulum-associated degradation) and in cell-cycle regulation; Lys-29-linked is involved in lysosomal degradation; Lys-33-linked is involved in kinase modification; Lys-48-linked is involved in protein degradation via the proteasome; Lys-63-linked is involved in endocytosis, and DNA-damage responses. Linear polymer chains formed via attachment by the initiator Met lead to cell signaling. Ubiquitin is usually conjugated to Lys residues of target proteins, however, in rare cases, conjugation to Cys or Ser residues has been observed. When polyubiquitin is free (unanchored-polyubiquitin), it also has distinct roles, such as in activation of protein kinases, and in signaling By similarity. Ref.5 Ref.6

NEDD8-like protein RUB1: Appears to function as a stable post-translational protein modifier. An AMP-RUB1 intermediate is formed by an activating enzyme, distinct from the ubiquitin activating enzyme E1, which is composed of a heterodimer AXR1/ECR1. Auxin response is mediated, at least in part, through modification of the cullin AtCUL1 by the attachment of RUB1 to 'Lys-692'. Ref.5 Ref.6

Subunit structure

NEDD8-like protein RUB1: Forms a thiol ester with the heterodimer AXR1/ECR1, specifically with the 'Cys-215' of ECR1.

Subcellular location

Ubiquitin: Cytoplasm By similarity. Nucleus By similarity.

Tissue specificity

Expressed in leaves, stems and flowers. Ref.8

Miscellaneous

Ubiquitin is encoded by 16 different genes. Ubiquitin is generally synthesized as a polyubiquitin precursor with tandem head to tail repeats. Often, there is one to three additional amino acids after the last repeat, removed in the mature protein. Alternatively, ubiquitin extension protein is synthesized as a single copy of ubiquitin fused to a ribosomal protein (either L40 or S27A) or to a ubiquitin-related protein (either RUB1 or RUB2). Following translation, extension protein is cleaved from ubiquitin.

Sequence similarities

Belongs to the ubiquitin family.

Contains 2 ubiquitin-like domains.

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 7676Ubiquitin
PRO_0000396910
Chain77 – 15276NEDD8-like protein RUB1
PRO_0000035965
Propeptide153 – 1564 Probable
PRO_0000035966

Regions

Domain1 – 7676Ubiquitin-like 1
Domain77 – 15276Ubiquitin-like 2

Amino acid modifications

Cross-link11Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) Ref.7
Cross-link29Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) Ref.7
Cross-link33Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) Ref.7
Cross-link48Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) Ref.7
Cross-link63Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) Ref.7
Cross-link76Glycyl lysine isopeptide (Gly-Lys) (interchain with K-? in acceptor proteins) By similarity
Cross-link152Glycyl lysine isopeptide (Gly-Lys) (interchain with K-? in acceptor proteins) By similarity

Secondary structure

.............. 156
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
Q9SHE7 [UniParc].

Last modified August 10, 2010. Version 3.
Checksum: FA8D702BB9C1B3AE

FASTA15617,397
        10         20         30         40         50         60 
MQIFVKTLTG KTITLEVESS DTIDNVKAKI QDKEGIPPDQ QRLIFAGKQL EDGRTLADYN 

        70         80         90        100        110        120 
IQKESTLHLV LRLRGGTMIK VKTLTGKEIE IDIEPTDTID RIKERVEEKE GIPPVQQRLI 

       130        140        150 
YAGKQLADDK TAKDYNIEGG SVLHLVLALR GGFGLL 

« Hide

References

« Hide 'large scale' references
[1]"Sequence and analysis of chromosome 1 of the plant Arabidopsis thaliana."
Theologis A., Ecker J.R., Palm C.J., Federspiel N.A., Kaul S., White O., Alonso J., Altafi H., Araujo R., Bowman C.L., Brooks S.Y., Buehler E., Chan A., Chao Q., Chen H., Cheuk R.F., Chin C.W., Chung M.K. expand/collapse author list , Conn L., Conway A.B., Conway A.R., Creasy T.H., Dewar K., Dunn P., Etgu P., Feldblyum T.V., Feng J.-D., Fong B., Fujii C.Y., Gill J.E., Goldsmith A.D., Haas B., Hansen N.F., Hughes B., Huizar L., Hunter J.L., Jenkins J., Johnson-Hopson C., Khan S., Khaykin E., Kim C.J., Koo H.L., Kremenetskaia I., Kurtz D.B., Kwan A., Lam B., Langin-Hooper S., Lee A., Lee J.M., Lenz C.A., Li J.H., Li Y.-P., Lin X., Liu S.X., Liu Z.A., Luros J.S., Maiti R., Marziali A., Militscher J., Miranda M., Nguyen M., Nierman W.C., Osborne B.I., Pai G., Peterson J., Pham P.K., Rizzo M., Rooney T., Rowley D., Sakano H., Salzberg S.L., Schwartz J.R., Shinn P., Southwick A.M., Sun H., Tallon L.J., Tambunga G., Toriumi M.J., Town C.D., Utterback T., Van Aken S., Vaysberg M., Vysotskaia V.S., Walker M., Wu D., Yu G., Fraser C.M., Venter J.C., Davis R.W.
Nature 408:816-820(2000) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: cv. Columbia.
[2]The Arabidopsis Information Resource (TAIR)
Submitted (APR-2011) to the EMBL/GenBank/DDBJ databases
Cited for: GENOME REANNOTATION.
Strain: cv. Columbia.
[3]"Empirical analysis of transcriptional activity in the Arabidopsis genome."
Yamada K., Lim J., Dale J.M., Chen H., Shinn P., Palm C.J., Southwick A.M., Wu H.C., Kim C.J., Nguyen M., Pham P.K., Cheuk R.F., Karlin-Newmann G., Liu S.X., Lam B., Sakano H., Wu T., Yu G. expand/collapse author list , Miranda M., Quach H.L., Tripp M., Chang C.H., Lee J.M., Toriumi M.J., Chan M.M., Tang C.C., Onodera C.S., Deng J.M., Akiyama K., Ansari Y., Arakawa T., Banh J., Banno F., Bowser L., Brooks S.Y., Carninci P., Chao Q., Choy N., Enju A., Goldsmith A.D., Gurjal M., Hansen N.F., Hayashizaki Y., Johnson-Hopson C., Hsuan V.W., Iida K., Karnes M., Khan S., Koesema E., Ishida J., Jiang P.X., Jones T., Kawai J., Kamiya A., Meyers C., Nakajima M., Narusaka M., Seki M., Sakurai T., Satou M., Tamse R., Vaysberg M., Wallender E.K., Wong C., Yamamura Y., Yuan S., Shinozaki K., Davis R.W., Theologis A., Ecker J.R.
Science 302:842-846(2003) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
Strain: cv. Columbia.
[4]"Large-scale analysis of RIKEN Arabidopsis full-length (RAFL) cDNAs."
Totoki Y., Seki M., Ishida J., Nakajima M., Enju A., Kamiya A., Narusaka M., Shin-i T., Nakagawa M., Sakamoto N., Oishi K., Kohara Y., Kobayashi M., Toyoda A., Sakaki Y., Sakurai T., Iida K., Akiyama K. expand/collapse author list , Satou M., Toyoda T., Konagaya A., Carninci P., Kawai J., Hayashizaki Y., Shinozaki K.
Submitted (JUL-2006) to the EMBL/GenBank/DDBJ databases
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
Strain: cv. Columbia.
[5]"The ubiquitin-related protein RUB1 and auxin response in Arabidopsis."
del Pozo J.C., Timpte C., Tan S., Callis J., Estelle M.
Science 280:1760-1763(1998) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION, INTERACTION WITH AXR1 AND ECR1.
[6]"The Arabidopsis cullin AtCUL1 is modified by the ubiquitin-related protein RUB1."
del Pozo J.C., Estelle M.
Proc. Natl. Acad. Sci. U.S.A. 96:15342-15347(1999) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION.
[7]"Multidimensional protein identification technology (MudPIT) analysis of ubiquitinated proteins in plants."
Maor R., Jones A., Nuehse T.S., Studholme D.J., Peck S.C., Shirasu K.
Mol. Cell. Proteomics 6:601-610(2007) [PubMed] [Europe PMC] [Abstract]
Cited for: UBIQUITINATION [LARGE SCALE ANALYSIS] AT LYS-11; LYS-29; LYS-33; LYS-48 AND LYS-63.
Strain: cv. Landsberg erecta.
[8]"The rub family of ubiquitin-like proteins. Crystal structure of Arabidopsis rub1 and expression of multiple rubs in Arabidopsis."
Rao-Naik C., delaCruz W., Laplaza J.M., Tan S., Callis J., Fisher A.J.
J. Biol. Chem. 273:34976-34982(1998) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (1.7 ANGSTROMS) OF 79-152, TISSUE SPECIFICITY.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
AC007654 Genomic DNA. Translation: AAF24594.1.
CP002684 Genomic DNA. Translation: AEE31344.1.
BT005749 mRNA. Translation: AAO64156.1.
BT006110 mRNA. Translation: AAP04095.1.
AK228591 mRNA. Translation: BAF00506.1.
PIRC86439.
RefSeqNP_564379.2. NM_102873.4.
UniGeneAt.25337.
At.30783.
At.43046.

3D structure databases

PDBe
RCSB-PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
1BT0X-ray1.70A77-152[»]
ProteinModelPortalQ9SHE7.
SMRQ9SHE7. Positions 1-152.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

BioGrid25258. 3 interactions.

Proteomic databases

PaxDbQ9SHE7.
PRIDEQ9SHE7.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblPlantsAT1G31340.1; AT1G31340.1; AT1G31340.
GeneID840023.
KEGGath:AT1G31340.

Organism-specific databases

TAIRAT1G31340.

Phylogenomic databases

eggNOGCOG5272.
KOK12158.
OMAKNSNKEQ.
PhylomeDBQ9SHE7.

Gene expression databases

GenevestigatorQ9SHE7.

Family and domain databases

InterProIPR019956. Ubiquitin.
IPR000626. Ubiquitin-like.
IPR029071. Ubiquitin-rel_dom.
IPR019954. Ubiquitin_CS.
[Graphical view]
PfamPF00240. ubiquitin. 2 hits.
[Graphical view]
PRINTSPR00348. UBIQUITIN.
SMARTSM00213. UBQ. 2 hits.
[Graphical view]
SUPFAMSSF54236. SSF54236. 2 hits.
PROSITEPS00299. UBIQUITIN_1. 2 hits.
PS50053. UBIQUITIN_2. 2 hits.
[Graphical view]
ProtoNetSearch...

Other

EvolutionaryTraceQ9SHE7.

Entry information

Entry nameRUB1_ARATH
AccessionPrimary (citable) accession number: Q9SHE7
Secondary accession number(s): O80715 expand/collapse secondary AC list , P59263, Q0WQU3, Q38875, Q9LDJ2, Q9LYW1, Q9M0W3, Q9M1P9, Q9S7X3
Entry history
Integrated into UniProtKB/Swiss-Prot: October 31, 2003
Last sequence update: August 10, 2010
Last modified: July 9, 2014
This is version 101 of the entry and version 3 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programPlant Protein Annotation Program

Relevant documents

SIMILARITY comments

Index of protein domains and families

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

Arabidopsis thaliana

Arabidopsis thaliana: entries and gene names